Draft Genome of a Type 4 Pilus Defective Myxococcus xanthus Strain,
Susanne Müller,aJonathan W. Willett,bSarah M. Bahr,aJodie C. Scott,cJanet M. Wilson,dCynthia L. Darnell,aHera C. Vlamakis,e
John R. Kirbya
Department of Microbiology, University of Iowa, Iowa City, Iowa, USAa; University of Chicago, Department of Biochemistry and Molecular Biology, Chicago, Ilinois, USAb;
The Forsyth Institute, Department of Microbiology, Cambridge, Massachusetts, USAc; Division of Select Agents and Toxins, Office of Public Health Preparedness and
Response, Centers for Disease Control and Prevention, Atlanta, Georgia, USAd; Harvard Medical School, Department of Microbiology and Immunobiology, Boston,
S.M., J.W.W., and S.M.B. contributed equally to this work.
Myxococcus xanthus is a member of the Myxococcales order within the deltaproteobacterial subdivision. Here, we report the
Received 9 May 2013 Accepted 13 May 2013 Published 20 June 2013
Citation Müller S, Willett JW, Bahr SM, Scott JC, Wilson JM, Darnell CL, Vlamakis HC, Kirby JR. 2013. Draft genome of a type 4 pilus defective Myxococcus xanthus strain, DZF1.
Genome Announc. 1(3):e00392-13. doi:10.1128/genomeA.00392-13.
Copyright © 2013 Müller et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to John R. Kirby, firstname.lastname@example.org.
described in the late 19th century for their capacity to produce
macroscopic sporangioles or fruiting bodies (1). Organization
tion of two genetically distinct motility systems (2–29). Previ-
ously, the sequence of M. xanthus strain DK1622 was determined
(NC_008095.1) (30). Recently, we sequenced strain DZ2 (31).
These two laboratory strains are noted for behavioral differences
(2, 32, 33), and DZ2 has a larger genome (31).
M. xanthus DZF1 is directly descended from the intermediate
strain DK101, the progenitor for DK1622, and displays reduced
capacity for type IV pilus (T4P)-mediated motility. An earlier
study (34) mapped two point mutations in DK101 to pilQ, which
encodes the T4P secretin (G741S/N762G), accounting for some
have been noted, we sequenced DZF1 to determine if the addi-
relative to the progenitor.
M. xanthus DZF1 was sequenced at the University of Iowa
mosomal DNA was prepared as described previously (31) and
processed for sequencing following established protocols. The re-
sulting sequence comprises 388,477 reads totaling 249 Mb, repre-
75 contigs using Newbler software version 2.7. The resulting ge-
nome is approximately 9.28 Mb, similar to that for DZ2 (31), and
is approximately 147 kb larger than the DK1622 genome. The
RAST annotation server (35) predicts a total of 7,704 coding se-
quences (CDS) within the DZF1 genome.
The M. xanthus DZF1 sequence reveals a single nucleotide
yxococcus xanthus is a soil-dwelling deltaproteobacterium
with a genome length of ?9.2 Mb. The Myxococcales were
tution, but lacks the N762G substitution found in DK101 (34).
The impact of these SNPs has not been systematically determined
but affects the interpretation of several previous studies. Indeed,
deletion of mazF (encoding RNA interferase as part of a toxin-
antitoxin system) is synthetic with the pilQ allele in both DZF1
and DK101 to affect cell death (36, 37).
Current analysis is ongoing to determine the role of genes
found in DZF1, but not in DK1622, encoding proteins predicted
acid modification, and protein transport. Homologs to these
genes are found in DZ2 as well as other myxobacteria, including
Myxococcus fulvus, Stigmatella aurantiaca, and Sorangium cellulo-
sum. The presence of sequences unique to both DZF1 and DZ2,
while absent from DK1622, has been verified by PCR. Thus, the
differences between DK1622 and both DZ2 and DZF1 are attrib-
UV mutagenesis of DK101, which led to excision of one large
prophage (38, 39) and may have induced additional lesions. We
are investigating several unique sequences found in DZF1 and
DZ2 for their role in M. xanthus biology.
Nucleotide sequence accession number. This whole-genome
der the accession number AOBT00000000. The version described
in this paper is the first version.
Support for this work was provided by the University of Iowa and NSF
MCB-1244021 to J.R.K. Additional support for J.W.W. was provided by
NIH T32 GM077973.
We thank Tom Willett, Tom Bair, and Kevin Knudtson for helpful
discussions and data analysis.
Genome AnnouncementsMay/June 2013 Volume 1 Issue 3 e00392-13genomea.asm.org 1
the official views of NIH, NSF, or the University of Iowa.
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